A Different Life
by Holz9364
Summary: John Sheppard went on a suicide mission & mysteriously returns one year later to a very different Atlantis than he had left. How would you feel coming home to find someone else leading your team & dating the woman you love? Would you feel replaced?
1. Dates & Surprises

**A Different Life**

"Evan, where are we going?" Elizabeth Weir laughed as she was dragged along a Lantian corridor blindfolded.

Evan Lorne grinned, "It's a surprise Elizabeth, you'll just have to wait and see."

She sighed playfully as she was led through the empty halls of Atlantis until finally they stopped, "Happy birthday Elizabeth." He whispered as he untied the blindfold.

Elizabeth gasped at the site that beheld her when she opened her eyes, "Thank you so much." She grinned looking around the balcony. It was a small secluded balcony that only he and she knew about; they had found it on one of their walks and instantly fell in love with it. The balcony looked over the ocean and at this time when the sun was setting it was beautiful.

There was a small table set out on the balcony with two chairs and a selection of food and wine, it was simple, but she could not have asked for anything more.

Evan seemed relieved that she was satisfied with it and pulled out her chair for her; she gratefully took her seat and allowed him to pour her a glass of wine.

"To the easiest year we have had in Pegasus!" He toasted and with a light hearted smile she clinked her glass against his, although she did not entirely agree with his toast. For her it had been the hardest year by far in Pegasus.

"_John, you can't go! That planet is swarming with Wraith for crying out loud!"_

"_I have to Elizabeth! If I can damage them now when they are all together, this war could be won!"_

"_I can't let you do that John. It's a suicide mission."_

"_Maybe, but if it will save the lives of those I love I'm willing to take that risk."_

"_John…"_

"_Elizabeth, please."_

"_Go."_

"Elizabeth?" Evan frowned; she must have drifted into her thoughts for longer than she had thought.

She smiled at him, "I'm fine, I was just thinking about how much things have changed since this time last year."

He immediately understood, "Oh, the Colonel?"

She nodded, "He saved all of our lives Evan and sacrificed his own to do so. A toast to John Sheppard."

Evan raised his glass and clinked it against Elizabeth's, "To John Sheppard." He murmured, also emerged in memories.

"_Sir you've got out of worse than this before-"_

"_There's no chance I'm surviving this one Major. Just do one thing for me, look after Elizabeth."_

"_Colonel, I don't know if that will be necessary if you-"_

"_Major, just do it. Please."_

"_Yes sir."_

"Anyway lets not think about that tonight, it is your birthday after all and-"

"**Incoming traveller alert. Incoming traveller alert."**

Elizabeth frowned at Evan as the alarm sounded throughout the city and they both jumped up and hurried to the control. It took them less than 5 minutes to get there and when they did they were faced with a very confused Chuck, "It's Colonel Sheppard's IDC Ma'am."

Elizabeth and Evan exchanged a look of shock before Elizabeth ordered Chuck to lower the shield and hurried down to the control room with Evan at her heels.

It was only seconds, but the agonising wait for John to step through that gate felt like hours to Elizabeth, she dreaded him coming back, so much had changed now.

When he did step through the gate he looked the exact same as he had when he left, give or take a few scars and some stubble.

His eyes sought out Elizabeth and he walked over to her, enveloping her in a hug, "I never thought I'd see you again." He whispered.

Evan watched the exchange cautiously and was pleased when Elizabeth pulled away from John, "John…A lot has changed since you left."

It took less than 10 minutes to have AR-1 reunited with John in the Briefing room and Elizabeth sucked in a deep breath before telling John the news she knew he would hate to hear.

"After you successfully killed the Wraith, Earth's Stargate was destroyed and Atlantis was declared a colony."

John frowned, "You've been a colony for a year?"

Elizabeth nodded, "Of course that means there have been several marriages, even births. You've missed a lot." She smiled slightly.

Teyla nodded, "Yes John, myself and Ronon were married not long after you disappeared and we now have a very young child."

Evan smiled, "And their not the only ones. McKay even got married." He chuckled, "And to Major Cadman too."

Rodney rolled his eyes and Johns frown deepened, "Major Cadman?"

Elizabeth nodded, this part was gonna piss him off, "Yes. She leads AR-2. After you had been gone for a few months we needed a higher ranking officer so Major Lorne is now Lt Colonel Lorne and Laura took his place as Major."

John looked slightly annoyed, "Lt Colonel Lorne, so he outranks me?"

"No John, you have the same rank. We thought you were dead remember? You left us all hanging and didn't come back for a year. Life went on here John; we had to move on with our lives without you!" She retorted angrily, tears welling up in her eyes as she said it.

Evan reached across the table and took her hand, squeezing it to comfort her. Elizabeth only closed her eyes and shook her head. John stared at their joined hands, the hurt clear on his face.

Rodney sighed, "Like Elizabeth said, things have changed. She's going to be Dr Lorne soon."

John yelled out angrily and hit the table before storming from the room.

It was clear to the others that Elizabeth needed time alone; she was trying very hard to hold back her tears. Evan nodded to them to signal they were dismissed as he wrapped his arms around Elizabeth and held her tight.

Meanwhile John stood alone on the balcony he had always shared with Elizabeth, he wiped at his eyes angrily, frustrated at himself for ever caring so much. This was not the life he had left and it wasn't the one he wanted to live either.

**To be continued?**


	2. Broken Hearts & Promotions

**A Different Life**

**Chapter 2**

"Do you mind if I join you?"

"Yes."

"John-"

"Elizabeth I'm sorry, but you are the last person I want to talk to right now."

Elizabeth could hear the anger and hurt in his voice as he spoke, refusing to turn and face her, always keeping his gaze on the ocean. She sighed, she had hoped he had calmed down and that she might be able to get through to him, clearly she was wrong.

"I'm sorry for bothering you." With that the doors swished open and closed again, she was gone.

John let out a sigh and released the tension in his body that he hadn't even been aware he was holding in that moment she was with him, he knew he shouldn't be acting in the way that he was, but it was perfectly reasonable after coming home to find that Lorne had completely replaced him in _EVERY _aspect of his life, well what _HAD_ been his life rather.

He had been standing out here for of a couple of hours now, not wanting to leave because he didn't know where to go. What had happened to his quarters and belongings? Were they gone? He just didn't know.

As if hearing his thoughts the door swished open once more and a familiar gentle voice said, "John, your quarters are exactly the way you left them."

John turned to face her, "You didn't get rid of all my stuff?"

Teyla shook her head, watching him closely, "No. Elizabeth kept everything exactly as you left it so that if you returned it would be there for you to go back too. Do you remember where your quarters are?"

John smiled at the woman's attempt to walk him to his quarters, she clearly had something to tell him, "Yeah, but you can walk with me anyway, I need the company."

She smiled warmly at him and they walked from the balcony together, John glanced quickly through the control room to Elizabeth's office (out of habit more than anything else really) where he saw her pacing as Lorne sat on her desk. His eyes darkened as he saw Lorne sitting there, where he had always sat. This notion however did not go un-noticed by Teyla.

When they were in the safety of the quiet hallways she dared to speak, "She went there every night for the first 3 months."

John frowned, "Who went where?"

Teyla looked at him intensely, "Elizabeth. She slept in your quarters for the first 3 months, everything still smelled of you and... well it kept her sane. John, if Lt Colonel Lorne had not stepped in and helped her I dread to think what would have happened to-"

"Yeah, Yeah I get it Teyla. She thought I was dead and Lorne stepped in to save the day, I know. Doesn't make it any easier though." He added the last part quietly and Teyla pretended she hadn't heard him, but John knew she had.

"Well here we are, home sweet home. Thanks Teyla." John said politely, but Teyla knew it to be a dismissal so with a nod she turned and walked back in the direction they had come. John watched her walk away thoughtfully and only opened the door to his quarters once she was out of sight.

Teyla had been right about his quarters, everything was the way he had left it, but something was different... someone had made his bed. With a sigh he pulled off his jacket, boots and socks and lay down on his bed, hoping to get some well needed sleep. It was then that he noticed something that distracted him, his bed smelt of Elizabeth, her perfume, her scent. He breathed it in with a sad smile, she had moved on now, things between them would never be the same again.

**Meanwhile in Elizabeth's Office:**

Elizabeth had been pacing anxiously for about 10 minutes before she eventually spoke, "What the hell are we gonna do?"

"Well Carson says he's fine physically. Mentally, on the other hand not so much because we have no idea what he's gone through so I guess he is fine to be re-instated as soon as Carson gives the go ahead." Evan said thoughtfully.

"Re-instated? Evan how are we going to re-instate him? _You're _my 2IC now, I can't just un-promote you!" She cried out as she continued to pace the office furiously.

Evan sighed, "He was your 2IC before I was Elizabeth and we both know he was a hell of a lot better than me. Put him back in charge of AR-1, give me my old team, AR-2 back, I get on great with them. He belongs in this position, not me and we both know it.

When Elizabeth caught his eyes that was when she knew that he understood exactly what was going through her head at that exact moment. The pain she saw in his eyes told her everything she needed to know, he _KNEW._

"Is it really as easy as that?" Elizabeth asked with a frown.

Evan shrugged, "We're a colony Elizabeth, you're essentially in charge of everything, so yes it is that easy."

She groaned, "Is it the right choice? Will it change things between us?"

Evan stood up at that, "Yes it is the right choice, I back you up and want you to re-instate him. As for whether or not things will change, I think we both know that they will now that the Colonels back."

Then with one last look, a look full of pain and sadness, a look that wrenched Elizabeth's heart out of her chest, he left.

She watched him walk away until he had left the control room and was out of her sight, then she looked down at the simple engagement ring she wore on her finger and twisted it anxiously. Evan was right; everything was going to change now.

**The Next Day:**

_BLEEP. BLEEP. BLEEP. BLEEP._

John groaned and tried to bury his face deeper into his pillow, why would someone be at his door this early in the morning.

_BLEEP. BLEEP. BLEEP_

"Alright! I'm up!!" He shouted in annoyance as he jumped up and quickly put on some clean clothes_, _ran a hand through his hair then answered the door to find Rodney standing outside.

"Hi." He said, somewhat awkwardly.

John smiled, glad to see a familar face even if it was Rodneys, "Hey McKay."

"Um, well I thought you might want to go get breakfast? And there's a meeting after which you've gotta be at. Good news for you though so your gonna want to go." He said, still a little awkwardly, it had been a long time since they had spoken and John knew what Rodney was like.

"It doesn't sound like I have a choice." He said stepping out of the doorway and heading towards the mess, Rodney walked along next to him and with a sigh John asked, "So is there anyone here who isn't married?"

Rodney (as John knew he would) seemed to return to his ordinary self at the mere mention of gossip, "Well Elizabeth and Lorne aren't yet, but that's meant to happen soon, mind you they had a bit of a bust up in her office yesterday so…"

John never heard the rest of Rodney's rambled story, his eyes brightened at the fact Elizabeth and Lorne had, had an argument, maybe, just maybe there was hope for him yet -

"Sheppard! Sheppard, are you even listening?" Rodney asked, John had clearly irritated him.

"Sorry Rodney, my mind was elsewhere." He said as they entered the mess hall. John's eyes immediately sought out Elizabeth who sure enough was sitting at a table alone.

Rodney seemed to notice this too because when they had gotten their food he walked over to Elizabeth's table and asked, "Is it okay if we sit with you Elizabeth?"

She hadn't heard them approaching and looked up from her coffee a little startled, before giving him a small nod as her eyes locked with Johns, from that look she could tell he was thinking exactly what she was; Can things ever be the same now? It was an unanswered question that would probably always remain that way.

"Where's your other half today" Rodney asked conversationally, John knew he was just fishing for gossip.

Elizabeth frowned, not once looking up from her coffee, "Evan? I'm not sure. He wasn't in our quarters last night after the argument."

"What was the argument about?" John asked curiously and Elizabeth's frown deepened as she looked up and set her gaze on him, "You." She said quietly, causing him to frown along with her.

Before he could say anything else however she just shook her head and said, "You'll understand at the meeting." She stood to leave and with a small, forced smile said she would see them later and bade them enjoy the rest of their breakfast.

John ate silently as Rodney watched him, trying to figure out why he had changed so much probably, if anyone knew what had happened on that planet they would understand, but it wasn't a story he felt like telling anyone anytime soon.

**The Meeting:**

John and Rodney were the last ones to enter the Briefing Room and John surveyed the room closely. At the end of the table sat Elizabeth, like she always did and next to her were 2 empty seats. Those were the seats he and Rodney had always occupied, but at the first meeting Lorne had sat in what had always been his seat. Next to Rodney's empty seat sat Teyla as usual and next to his, Ronan. Then next to Teyla was Lorne, John had deja-vu to the AR-1 / 2 meetings because Laura Cadman also sat on Ronan's other side.

Rodney took his place on Elizabeth's left hand side and John on her right, he was still confused about why he was there, in that room and in that seat, until Elizabeth spoke.

"Things are going to change a little around here everyone. I have put some serious thinking into this decision, but I think it is the right one." She looked around the table at many curious faces, all but Rodney and Lorne's; they were obviously in on this little secret.

"I have decided to re-instate Lt Colonel Sheppard as my second in command and I would like to promote him to Colonel. If he accepts." She turned to John anxiously searching his face for any sign of happiness, at that moment all she could see was shock, but then to her relief that familiar flyboy grin spread across his face, "I get my team back?" He asked eagerly and Elizabeth chuckled with joy, the old John Sheppard was back.

"Of course you get your team back. They wouldn't have it any other way." Elizabeth told the man happily, at these words Rodney hi-fived John and Ronan and Teyla simply beamed at each other.

"Lt Colonel Lorne will once again be leading AR-2 and Major Cadman will be in charge of AR-3, if you both accept."

Lorne only nodded and Laura smiled, "Yes, ma'am."

She turned back to John whose gaze she had felt on the back of her head and they locked eyes like they had in the mess hall. He grinned at her, that lopsided grin she had missed so much and she couldn't help but laugh at how happy he was, laugh with joy at the fact he was here with her alive and well and happy.

The look meant more than it seemed to the average person, but everyone in that room knew John and Elizabeth well enough to understand it. Which is why Evan Lorne stood up and left the room without further ado and it was guilt that caused Elizabeth Weir to stand up, quickly excuse herself and hurry after him.

**To Be Continued. **


	3. MakeUps & Old Friends

**A Different Life**

**Chapter 3**

"You're acting childish about this, if you stopped interrupting and actually listened to me then maybe-"

"I don't want to speak to you right now. Frankly I'm not sure if I ever want to speak to you again Elizabeth, you and I both know what that look meant-"

"It meant nothing Evan! It was a look, simply a look."

"C'mon Elizabeth, I'm not stupid. It was so much more than a look, everyone knows you and the Colonel had a thing before-"

"Stop! Just stop, whatever happened between me and John in the past is irrelevant because it's in the past. This is the present and in the present _you _are my fiancée and the man I love Evan."

"Do you mean it or are you forcing yourself to say it? Because if you love him then leave me right now and save me the pain of marrying a woman who can never love me in the way that I love her."

They stood there, staring at each other for quite some time before Elizabeth enveloped him in a hug and whispered, "I want to marry you."

John had been standing in the shadows watching this exchange sadly and crestfallen he walked away. He knew it was because he left that this was happening, but that didn't make it his fault, if he hadn't left everyone would be dead. He wandered the corridors aimlessly, just feeling sorry for himself and wishing that Elizabeth would suddenly realize she loved him and come running onto the balcony into his arms. As he walked his fantasies became wilder and less realistic so by the time he walked into something and sent it flying to the floor his mind was in a church shouting "I OBJECT!" and singing the good old Busted song, 'Crashed the Wedding.'

Nevertheless he was drawn back into the real world by the collision. John bent down to help the woman up and it was then he realized who it was, "Ruby Mills?" He asked, eyes wide in shock as he helped her up. She stared at him just as shocked then laughed, "John Sheppard."

John grinned, "It's been years! Imagine meeting you again in the lost city of Atlantis."

Ruby nodded, "I must admit, I'm surprised to see you here too."

"So, I was about to go to the mess, wanna have lunch and catch up?" John asked eagerly causing Ruby to laugh, "John you were heading in the opposite direction of the mess hall." She pointed out.

John smiled at her sheepishly, "Well I just realized I was hungry."

"Sure, I'll join you." She told him and still smiling she began to walk with him, "So, you got pretty far with the air force then-" she looked at his jacket, "Lt Colonel."

John shrugged, "Ah I suppose so, getting promoted to Colonel soon." He told her with a cheeky grin, "Anyway, when did you get here?"

"3 days ago on the Daedalus, what about you? I haven't seen you around."

"I just got back yesterday, I've been away for a year, presumed dead act-"

"So you're the guy they all talk about!" Ruby exclaimed suddenly coming to a halt as they waited in line for food at the mess hall.

John frowned, "They talk about me?"

Ruby smiled and nodded, "Well yeah, it's a long story I'll explain it when we sit down." They waited in line talking about what they had been up to since the last time they had seen each other and it was then that John noticed that Ruby was the complete opposite of Elizabeth.

Ruby Mills was drop dead gorgeous, flawless skin and long blonde hair, perfect smile and an all round sweet girl. That made her sound like a bimbo, but she was a very bright scientist and she had been his first ever girlfriend, well proper relationship I suppose you would call it. Elizabeth didn't have flawless skin, she had freckles, but he loved them because he thought they were so cute. She never had perfect blonde hair either, but he loved the way her curls bounced as she walked away from him, shaking her head in amusement usually. He loved Elizabeth's smile too, he loved everything about Elizabeth come to think of it and they never had a normal relationship, hell it wasn't even really a relationship. Things were different now, they were a colony, there were no REGS, but it was too late.

"John?"

The sound of his name pulled him out of his thoughts and he saw Ruby looking at him with a frown, "You okay?"

He nodded, "Yeah, I'm fine. Got lost in thought, sorry. Let's sit over there."

Ruby could tell he didn't want to talk about it and they walked towards the table together, a few tables away sat Elizabeth and Lorne. John couldn't hear what they were saying, but he could see them talking and smiling which was really enough to put him off his lunch.

"So, like I was saying. You're the talk of the rumour mills on the Daedalus and the ones here as well from what I've heard." She cocked her head at him and he nodded to tell her to keep going, "Well you left for a suicide mission and you know the leader here she apparently had an emotional breakdown for a bit because there was some kinda thing going on there that was against the rules."

John frowned, the rumour mill had actually got it right for once and John was sick of keeping his emotions to himself. Ruby had helped him through the hardest moments in his life and he knew he could trust her, "It's a long story."

Ruby smiled, "I've got the afternoon off, you've been doing it again John, keeping things bottled up like that, and it's not healthy."

He nodded, "I know. Okay Ruby, Elizabeth and I had a 'thing' I suppose you could call it. It was a secret 'thing' and it wasn't a relationship, it was more of a friendship with strings attached."

She nodded, "Sex basically?"

John chuckled at her no nonsense attitude, "It started out that way until-"

"You fell in love with her." Ruby finished for him, "You know me too well." He muttered and she only smiled, "You're easy to read."

"So when did it start?" She asked him, out of curiosity rather than anything else probably.

"About 2 years before I left for the mission. We were friends to begin with and when I nearly died a few weeks after being there we became closer friends then there was a suicide mission I somehow managed to survive and when I came back we realized we needed each other and so it began." John rubbed his forehead and sighed, he could feel a major migraine coming on.

"So after being gone for a year, you came back and you still love her?" Ruby asked, trying to catch up to where they were in the present.

"Well when I was gone I went through hell and I came back expecting… to be honest I don't know what I expected. She thought I was dead, but I guess I just hoped that -"

"You would come back to find her waiting for you?"

"Yeah, would you stop doing that!" Ruby only smiled, "Continue."

"It doesn't matter anyway, I came back to find her engaged to Lorne." John said, sending a glare Lorne's way for good measure.

Ruby sighed, "Well, you're fucked."

John couldn't help, but laugh, "Thanks for pointing out the obvious. Anyway, enough about me. What are you doing here?"

"I'm a Scientist." She said with a strange sly smile.

John rolled his eyes, "I know that much, but I meant how did you end up here, in Atlantis?"

"I worked at the SGC for a while and I heard about this mission, I applied for the job as a Scientist to replace a man who had resigned, Kavanagh I think his name was and I got the job so here I am." She finished, still smiling.

"I like you much better than Kavanagh, he was an absolute ass. So how are you liking working with Rodney McKay?" John asked, chuckling as he waited for the groan that came from Scientists when he mentioned the name.

Instead Ruby just kept smiling, that lovely pleasant smile, "I like him, he's a good boss and a smart man, he's just misunderstood."

"Sometimes I wonder why you never became a shrink." John said, shaking his head at the woman who only laughed, "I'm good at understanding people that's all, plus I've known you for years John."

"There is that, so how have you been, met anyone over the years?"

She shrugged, "I was engaged for a couple of years, but it fell apart not long before I came here. I met this guy on the Daedalus though he's a doctor. He's been here since the start, but he was going back to Earth for family business, he's such a sweet guy -"

"Carson Beckett?" John asked with a smile, Carson was alive and with them once more after his presumed death, well his death. Their Carson was a clone, but Carson all the same.

She laughed, "Now whose reading who? Yes, do you know him?"

He nodded, "He's a nice guy, I've been here from the start too, we're all pretty close."

She frowned, "Who has been here from the start?"

John mirrored her frown as if deep in thought, "Me, Elizabeth, Carson, Rodney, Chuck, Radek… There were more, but … in the first few years here there were a lot of casualties and many close to us were killed. Ford and Grodin are two that I remember most, they had the biggest impact on us all."

Ruby leaned forward and placed her hand on his, "I'm sorry John. I know things have been difficult for you in the air force, but I hope that now things will start to look up again for you."

"John, you're in luck!" Ruby whispered and John frowned, he looked up from his coffee to see Elizabeth approaching. When he looked at her she gave him a nervous smile, "Hello Dr Mills, John do you have a moment?"

"Sure." John smiled at Ruby, "Thanks a lot for that Ruby, it was great to see you again."

Ruby nodded, "You too John."

He stood up and left the mess hall with Elizabeth, when they were alone in the corridor she checked to see if anyone was behind them then said, "John, we have to talk about what happened before you left."

**To Be Continued!**


	4. Arguments & Regrets

**A Different Life**

**Chapter 4**

John seemed confused that all of a sudden Elizabeth felt the need to talk about what had happened before the suicide mission, it seemed as though she wanted to put him and anything between them in the past.

John frowned, "Do you mind if we discuss this somewhere a little more private?"

Elizabeth raised an eyebrow at the man, "John, I'm not sure that's a good idea with our-"

He cut her off, "Elizabeth, it's just talking." The intense look he gave her must have convinced her that he was being truthful, his eyes pleaded with her. She knew he wanted to do more than talk and she knew it hurt him that talking was all he could do, but she felt sure that they he really meant, only talking.

So resigned to her fate she nodded, "We'll talk in your quarters, Evan isn't happy that I want to talk to you and since we share quarters I don't think going there would be such a good idea."

John nodded his agreement and in silence they walked towards John's quarters. He could tell Elizabeth was nervous from the way she kept wringing her hands and chewing on her lower lip, this talk was something neither of them were looking forward too.

When they finally reached Johns quarters (A walk that in reality lasted 5 minutes, but felt like 5 hours today) Elizabeth hesitated, John turned to her and sighed, "Just talking, I swear."

She gave him a small nod and entered his quarters after him; she swallowed hard as the door slid shut behind them. It had been a long time since they had been alone in this room together and things were so different now, it scared her terribly.

She looked down at the ground, "John, I-"

At the same time he had started to say, "Elizabeth-"

They both chuckled nervously and John said, "You go first."

She nodded, "I know things are very different from the way you left them, but I hope having your team back will make it feel the same to you again."

John knew she was stalling around the topic she really needed to discuss with him, but he let her do so, "It will never feel the same to me Elizabeth. I have my team back, but there are other things I will never have again."

Elizabeth chewed harder on her bottom lip, "John…Before you left…I'm sorry about what you returned to."

John shook his head angrily, "Sorry just doesn't cut it Elizabeth. I know you didn't expect me to come back and I know I didn't ask you to sit around and wait for me, but I got through hell on that planet by thinking about returning to you and I did not want it to be like this!"

Elizabeth's eyes swam with tears as she replied, in the same tone, "You think I wanted it to be like this John? Do you think I wanted you to return to find me engaged to the man who replaced you? It wasn't the way I envisioned you returning either, but 6 months went by and I gave up hope of every seeing you again."

"Does what happened before I left mean anything to you? Did you ever love me or was it only ever just the sex for you?" He yelled angrily at her, causing her to take one step closer to him, she had a dangerous look in her eyes.

"You think I never loved you? John _you_ left _me_ here! Okay, _not_ the other way around. I get it you had to save the world and all, but we could have avoided that attack."

John took a step towards her, shaking his head in anger once more, "No. The Wraith are gone now Elizabeth, it was worth that wasn't it? Surely it was worth something. I left you because I wanted to save you and everyone else on this damn base, not because I didn't love you!"

She looked as if she would burst into tears at any moment, but all the same Elizabeth kept her strong reserve, "John. I still have the ring and you can have it back, I never expected you to come back so when Evan proposed to me I-"

"You said yes and I presume you 'forgot' to tell Lorne you were already engaged." Elizabeth looked down, partly in shame and partly to hide her tears. When she looked up she had put on her façade as fearless leader once more, "I loved you John and it took a long time to let you go, I don't think I ever fully did, but you were gone and my life had to move on without you."

John nodded, "I get it, you loved me, but you love him now."

She made a small choking noise as she tried to swallow a sob before quietly saying to the floor, "I will never love him in the way that I love you and the worst part is, I think he knows that."

John raised his hands to the sky in frustration as he let out another angry yell, "Then why the hell are you marrying him? You should be marrying me! It was always you and me Elizabeth! Always."

"I know, but I can't hurt him anymore than I already have John, he's spent the last year living in your place and it's been hard enough without me leaving him now, after he's done so much for me." Elizabeth told the man sadly, not being able to keep eye contact with him throughout the whole conversation.

John just shook his head in disbelief as he turned his back to her and began to pace, "You are marrying him for all the wrong reasons Lizabeth, please don't do it."

She shook her head, it hurt her so much to hurt him this way, but it was the way things had to be, "I have to John." She all but whispered to him.

He shook his head and took another step closer to her, they were mere centimetres apart now and when Elizabeth let out a nervous sigh he could feel her breath hot on his neck, "No." He whispered, his hoarse voice sending shivers up her spine, "You don't."

John could tell Elizabeth was going to take a step back soon if he didn't do something about it, so he took her hands in his own and closed the space between them by covering her mouth with his own. Elizabeth resisted at first, but when her reserve cracked she melted into the kiss, her hands slipped out of his as she slid her arms around his neck, pulling him closer. The kiss had started out as a I-Need-To-Know-You-Still-Love-Me type of kiss and had quickly gone to more of a I-Want-You-Right-Now sort. A soft moan came from Elizabeth's mouth as John slid his hand up her shirt, her brain was too fuzzy to tell him to stop, the way he was kissing her told her how much he needed her and it made her feel guilty for ever thinking about marrying anyone other than him.

She knew as John pulled off her shirt and began to kiss her neck that her fiancé would be sitting in their quarters waiting for her, she knew that she shouldn't be here with John, but she still didn't feel compelled to leave, she wasn't going to leave, as much as she knew she should.

John's lips stopped for a moment and he whispered in her ear that he loved her; she knew she shouldn't have, but the words came to her on autopilot and she sighed, telling him that she loved him too.

Somehow they found their way to John's bed and Elizabeth felt that everything had returned so naturally now, it was like he had never left. It struck her that the way their bodies moved together so perfectly, in perfect sync, was so far from how she had felt whilst with Evan. She had closed her eyes and seen John to begin with and it had never felt as right as being with John did.

Elizabeth could not stop herself as she moaned his name over and over again and he kept whispering in her ear, telling her that he loved her. This was the most personal she and John had ever been. It had started as sex, but now, now it was so much more than that.

Elizabeth couldn't understand as she became closer and closer to the edge, what was holding her back, John was perfect in every single way and whilst Evan could satisfy her with marriage and the thought of a family, it all seemed ten times better with John.

She knew as she lay in his arms, breathing heavily with sweat glistening on her body that she couldn't do this. It was John or Evan and she knew what she wanted, but life was never that simple.

"Lizabeth?" He breathed from beside her, "Hm?" was her reply as she contemplated on how well and truly screwed she was.

"Do you love him?" John asked, she sighed, knowing what he wanted to hear was not the answer she was going to give him.

"Yes." She replied simply, causing Johns breathing to become faster, he was getting angry again.

"Then why? Why did you let me do that?" He asked her, the hurt and pain evident in his voice made her cringe.

"Because I needed to feel that again John, something that I only feel with you." She told him, sighing as she figured he would probably hate her for the rest of their lives; however he just kept asking questions.

"Are you going to marry him?" That question struck her hard, like a blow to the stomach. It was the one question she had been asking herself for the 3 days since John had returned. She didn't know how to answer and in the end she decided to tell him the truth. She snuggled closer into his bare chest and smiled slightly when his arm tightened protectively around her stomach.

"I don't know."

The words seemed to echo around the room and Elizabeth then decided she had to leave. She sat up and groped around in the dark for her clothes, as she quickly began to get dressed she heard John fall back onto the pillows with a sigh, "I didn't think you would stay." He stated and she knew that all along John had known she would never be able to stay the night; it would cause too many questions to arise. Nevertheless it didn't mean that he hadn't hoped that maybe, just maybe, she would have stayed.

Elizabeth pulled on her boots and stood up to leave, "This can't happen again John. I… I'm sorry."

She turned to leave and stopped when John spoke, so quietly that she almost never heard him, "I'm sorry too. Sorry that I ever messed up your life."

She turned and shook her head, "You never messed my life up. I messed it up myself."

Without another world she turned once more and left John's quarters. It was after midnight and luckily no one was out in the corridors, she didn't feel like going home just yet so she decided to take a detour to the McKay residence. When she buzzed on the door she smiled as she heard Rodney grumbling at Laura to get the door and then chuckled at the sound of her kicking him as she got up to see who was at the door at this late hour.

When she answered it, dressed in sweatpants and a vest top she smiled, "Hey Elizabeth, what brings you around here so late?"

Elizabeth shrugged, "I guess I just didn't really wanna go home. Did I wake you guys?"

Laura shook her head, "No, we were just watching 6th sense; Rodney wants to see how it ends." She rolled her eyes at her friend and asked if she wanted to stay the night in the spare room. Elizabeth gratefully accepted the offer and entered her friends' quarters.

Rodney gave her a wave and a small smile from where he lay in bed watching 6th sense on the small portable DVD player.

Elizabeth smiled back, "Hey Rodney, hope you don't mind, I'm crashing here tonight."

Rodney shook his head, "Nah, not at all, your practically family Elizabeth."

Laura chuckled as she led Elizabeth into the spare room, she rarely slept here now as it was on rare occasions that she fought with Evan, but things had been different before he had helped her out and the McKay residence had been her constant place of refuge. She had grown very close to Laura and had always thought of Rodney as a brother, it meant a lot to her that she was welcome here whenever she needed it.

Laura leant Elizabeth a spare nightgown from her closet and sat down next to her on the bed, "What happened with Evan?"

Elizabeth sighed and confessed to her friend, "It's not so much what happened with him, but more what happened with John."

Laura frowned, "So you talked to him about what happened before the mission then?"

Elizabeth nodded, "Yeah, only it ended up in…well…"

"Did you have sex with him?" Laura asked suspiciously and guilty she nodded.

Laura offered her friend a comforting smile, "Elizabeth, things will work out okay. Maybe you need to accept that things with Evan just won't be the same now."

"Break off the engagement you mean?" Elizabeth asked, causing Laura to shrug, "I can't answer that, it is your decision after all, but just think about it okay?"

Elizabeth nodded, "Yeah, thanks for letting me stay here Laura."

Laura opened her mouth to speak when Rodney shouted from the other room, "Movies finished Laura! You coming to bed?"

Laura called back, "Be right there Rodney!" She turned to Elizabeth, "It's fine Elizabeth. You can stay with us as long as you need too." With that she left the room.

Laura closed the door to the spare room behind her and quickly changed before getting into bed next to Rodney, "What's up with Elizabeth?" Rodney asked his wife quietly.

Laura sighed as she made herself comfy next to Rodney, "She slept with Sheppard." Laura whispered causing Rodney to make a, "humph." noise and quietly say that he wasn't surprised.

Laura rolled her eyes, although Rodney couldn't see it in the dark room, "Just get some sleep Rodney." she mumbled and he happily obliged.

In the spare room Elizabeth had changed and turned off the light. As she lay in bed she couldn't stop thinking about John and how right it had felt to be with him again, but then her thoughts spun around to Evan and how wrong it was to do that to him, how unfair it was and how out of character it had been for her to do such a thing.

She sighed and turned onto her side, she knew it was going to be a restless night. She closed her eyes and whispered to the dark room, "I'm sorry."

**To Be Continued!!**


	5. Abuse & Sickness

**A Different Life**

**Chapter 5**

After several hours of tossing and turning Elizabeth gave in. She glanced at the clock by the bedside; it was only half past 5. She had barely slept at all the whole night, her thoughts were in a whirlwind and the cogs in her brain just wouldn't stop turning. She sighed and got up from the bed, after quickly dressing into the clothes she had worn the day before and pulling her hair into a messy ponytail she was ready. She clicked on the desktop light and wrote a small note of thanks to the McKay's for letting her stay; she left it on their bedside table as she crept silently to the door and headed off down the corridor.

Elizabeth had been walking for about 5 minutes before she realised she was going the wrong way, she had turned left and now stood outside John Sheppard's quarters when what she should have done was turn right towards the quarters she shared with Evan, her _fiancé_, she reminded herself forcefully. It was with a grudged sigh that she turned around and began to walk back to her quarters. By the time she had retraced her path and made her way to her quarters it was still far too early for anyone to be up. It was Sunday after all and ever since Atlantis became a colony, everyone got Sunday off.

She knew Evan would still be fast asleep, it was only 5:45am and he usually slept till at least 9am on Sundays, sometimes even later. Naturally she wasn't surprised to walk into darkness when she entered the room, she tiptoed over to the bed to make sure that Evan was asleep and once satisfied that he was she slipped into the spare room adjoined to their sleeping quarters. The purpose of their spare room had been the same as the purpose of Rodney and Laura's, for Evan at least. It was there in case they decided to have children and needed a spare room. With Laura now 4 months pregnant the room would soon be spare no longer, but the spare room in the Lorne residence should really be renamed the 'junk room'.

When the pair had moved in together they realised they had too many possessions to fit into one room so anything that was not needed in everyday life had been dumped in the spare room, whenever Elizabeth had a moment she tried to tidy it out, but it would only end in disaster and the result was that the room would usually look worse than it had before she began.

However, it was with an intention she entered the spare room at this ungodly hour, she clicked on the light and headed for the chest of drawers that had sat in her quarters. In the bottom drawer was a box, it was buried under stacks of paperwork and old journals, but she knew its exact location.

She opened the box's lid and poured the contents onto the bed, there was one thing in particular she needed to see right now, the engagement ring. She smiled, somewhat sadly as she looked down at the ring John had given her when he proposed. She didn't know why she had kept it, she should have thrown it away, but she couldn't bring herself to do it so it ended up sitting in the box, along with all the pictures of John she owned, hidden away from her fiancé. There was no way that was right, she thought with a sigh. Grudgingly Elizabeth placed the ring back into its box with all the photo's, she didn't want to look at them now, so many happy memories from when everything had been okay, nothing was okay now. The box was put back in its hiding place for another few months, until she felt the need to venture into it in the dead of night and with a sigh Elizabeth clicked off the light and left the room.

When she re-entered her quarters it was only 6am and Evan was still fast asleep, it was only then that she noticed how tired she really was. She slipped into some comfy clothes that served as pyjamas and climbed into bed next to her fiancé. As the sun rose outside a stream of faint orange light shone into the room and illuminated his face, as she looked at him she felt a knot in her stomach tighten, she could never tell him about John, their entire life was going to be lived a lie.

She got a shock when Evan opened his eyes, "I thought you were asleep." She whispered quietly and he shrugged, "I didn't sleep very well last night, it feels odd without you next to me. Where were you last night Elizabeth?"

Elizabeth sighed and took his hand, "I was at Laura and Rodney's, I knew you were still mad and I thought it best to put some distance between us until you cooled down."

She sighed inwardly when he nodded in understanding, she was relieved he believed her lie, but it only made the guilt worse. Evan squeezed her hand and gave her a smile, "We're okay now though, aren't we?"

Elizabeth nodded, "Yes, we are. Although there was one thing I wanted to talk to you about."

He propped himself up on his elbow to get a better look at her, "Shoot."

Elizabeth bit her lip, not really sure of how to say this or what her excuse was going to be, she improvised, "I think we should post-pone the wedding. It's just things are hectic lately now that John's back. So many extra meetings and gate-calls with all these other worlds wanting to welcome him back as the saviour of mankind, I'm overworked."

Evan had nodded throughout her explanation and said, "I know, it's okay Elizabeth, we can post-pone the wedding for as long as you want. As long as you love me I'm a happy man." He told her with a grin, Elizabeth tried to respond with a light-hearted smile, but she felt sure that it came out more like a grimace, "Do you mind if I try and get some sleep? There are a few hours till morning and I really didn't get much last night." She told the man who yawned in response, "That sound's like a good idea, I'm shattered."

*

For the next few weeks following John's return and Elizabeth's act of impulse a void began to show between the leader and her 2nd in command. They barely spoke and it was obvious that Elizabeth was avoiding John; to begin with he tried to talk to her before giving up. He spent all his time with his team or his new personal shrink, Ruby. Elizabeth was never seen without Lorne and that was the way John had accepted it would have to be.

However, he felt compelled to speak to her one day in the mess hall, almost a month after he had returned. She entered the mess hall one morning without her other half and these days that had become very rare. From where John sat eating fruit loops with Ruby he watched her traipse into the room, grab some coffee and sit down alone at an isolated table in the corner.

He turned to Ruby frowning deeply, "She's not with Lorne and she looks really depressed."

Ruby shrugged, "They probably just had an argument. They'll be together again soon; those two seem joint at the hip lately,"

John grumbled something about how he had noticed causing Ruby to roll her eyes, "Would you get over the whole depressing ex-love thing? I wouldn't be too sure you have anything to worry about."

John stopped grumbling abruptly at this piece of news, "What? How? What happened? When did you he-"

She chuckled and held up a hand to stop him, "It's just intuition John, I don't think this engagement is going to work out."

John was only half-listening now as he watched Elizabeth, "Hm… Do you think I should go talk to her?"

Ruby smiled, "Sure. Just make sure the other half doesn't see you, if he walks in and sees that I don't think he will be too pleased with you."

John nodded, "Good point. Okay, see you at lunch Ruby."

"Good luck John." She told him with an amused smile as he stood up and practically jogged over to Elizabeth's table.

He smiled as he approached her, "Morning Elizabeth, could we talk?"

Elizabeth sighed, "Sure." She said, motioning at the seat across from her.

He sat down and looked over at her, it was the first time he had seen her properly all week, they hadn't had any meetings together and he was pretty sure she had been avoiding him, "I miss you. Be my friend again, please."

Elizabeth seemed shocked at his sudden revelation and feigned ignorance, "We are friends John, I've just been a little bit busy lately, what with all this-"

"No, you've been avoiding me Elizabeth. I know you have and I wish you wouldn't do it, or at least give me a reason." He interrupted, he wasn't shouting; in fact he hadn't even raised his voice. He just sounded hurt.

Elizabeth sighed once more and looked up for the first time since he had joined her at the table, "John, after what happened between us…I just don't want that to happen again and-"

"What happened to your face?" John asked in shock as he saw the angry purple bruise on Elizabeth's cheek, she shrugged, "I fell and hit my face on the bed. It's not as bad as it looks."

John narrowed his eyes at the woman sitting across from him, she could tell he didn't believe her excuse, "Elizabeth, you don't strike me as the clumsy type and you don't get a bruise like that from a fall."

Elizabeth opened her mouth to protest, but John took her shoulder in his hand and gently pulled her to stand up, "C'mon Lizabeth, we're going for a little walk."

Elizabeth rolled her eyes slightly, but got up anyway, "John, I'm fine, it's only a little bruise."

He raised an eyebrow at her, "A little bruise? Its bright purple and it looks down right sore."

John swiped his hand over the door panel and they walked out onto a nice small balcony that gave them a lovely view of the city, Elizabeth knew the fact he had brought her here was bad. He only brought her here when it was bad news because the door was lockable, unlike the other balconies, hence no one could listen in.

She crossed her arms and leaned against the balcony barriers, looking at John expectantly. John looked at her intensely, "If I guess right, just tell me so because I know you and I know I'm right, I just want you to admit it."

He looked at her for a few more seconds, "Lorne was drunk last night when he left movie night with the guys. My guess is he came home and you two had an argument."

Elizabeth nodded, "Yes, we argued because he had too much to drink, it was just a silly little argument John."

John shook his head in disbelief, "He hit you Elizabeth. I know he did."

Elizabeth looked down, in an attempt to put on her poker face and then something in her snapped and she gave up pretending to be strong when she wasn't. John could see straight through the act anyway so it really was pointless with him. "Yes, he hit me and I'm not going to defend him because I know he shouldn't have done it, drunk or not."

John opened his mouth eagerly, no doubt to tell her to ditch him and scrap the engagement and wedding plans, but Elizabeth shook her head and continued, "But, I am not calling off the engagement because he won't do it again. I'm not afraid of Evan, John."

John opened his mouth angrily, but then closed it again and groaned in frustration before turning and leaving the balcony. Elizabeth sighed sadly and turned towards the Ocean. She didn't know how all of a sudden in a few short weeks her life had turned upside down. She began to feel very sick and took deep breathes of fresh air, it didn't seem to make a difference and she felt sure she would be sick. Wondering why all of a sudden she had felt so queasy she hurried the short distance to her quarters and headed straight for the bathroom.

Evan, who had just finished getting dressed, heard her being sick, "Elizabeth, are you okay?"

"No." she called from the bathroom, "I'm ill Evan, can you ask John to cover for me today?"

Evan cringed as he heard the sounds of sickness again, "Okay. I'll come and check on you before my mission." He promised her before leaving to find John.

It took him nearly half an hour before he finally found the Colonel in Rodney's lab, "Colonel Sheppard." He said, somewhat stiffly.

John's eyes hardened as he saw who the man was, "What is it Lorne?"

Evan tried to be as polite as he could, "Elizabeth asks that you cover for her in her meetings today."

John frowned, "Why? I just spoke to her this morning, she seemed fine."

Evan mentally stored that fact that they had spoken this morning, he would have to ask Elizabeth about that one, "Well she's sick, can you cover for her today? My team have a mission."

John nodded, "Yeah, no problem."

Evan returned the nod, "Thank you, sir." He told the man and walked away as quickly as he could, the man he had once considered as a friend really infuriated him at times now.

At 1100 hours AR-2 headed out to ransack a Wraith outpost and John was left in charge. However, with Lorne gone the first thing he did was tell Chuck he wouldn't be long and headed to Elizabeth's quarters. He didn't use the buzzer, he just walked into her quarters and seemed quite shocked to see her lying in her bed, wrapped up in the quilt, but still shivering.

"Lizabeth." He said quietly and she frowned, recognising his voice straight away even though her back to him was turned.

"What do you need John? Is the city okay?" She asked shakily. John sat down on the edge of the bed, "The city is fine Lizabeth, I just needed to see if you were alright."

"I'll be fine John. I'm sure it must be something I've eaten." Elizabeth said, her teeth chattering as she spoke.

John frowned, "You sure Lizabeth? It's boiling in here and you're shivering. Maybe we should go get Carson."

"I just need some sleep John, I'm fine. I don't need to see Carson." She mumbled, he had to admit she did sound very tired. John could only see half of her face from where he sat, but she looked very pale and she was sweating, although she did have a point; her eyes looked very dark.

He decided to let her stay where she was for now, "Okay, but if you feel any worse when Lorne comes back tonight I'm ordering him to take you to the Infirmary and if he won't then I'm ordering Carson here, okay?"

Elizabeth nodded feebly, "Okay, I promise to tell Evan tonight if I feel the need to see Carson."

"Good. You know I'm just worried about you Lizabeth." He told her softly, watching her affectionately, his eyes full of worry.

A small smile tugged on Elizabeth's lips, as terrible as she felt she could count on him to cheer her up, "I know John, thank you."

He returned the small smile, "It's my job Lizabeth. Get better soon." he said, leaning over and placing a kiss on her forehead before leaving the room so she could get the sleep she so badly needed to catch up on.

*

John spent the whole day pacing Elizabeth's office, thinking up all the possible illnesses and diseases Elizabeth could have and waiting anxiously for Lorne to get back so that he could go check on Elizabeth. He found himself checking his watch for the thousandth time that day and was pleased to discover that it was 2 minutes before 1900 hours, the time that Lorne's team were due to return.

As if sensing his thoughts the gate activated and Chuck yelled, "Lt Colonel Lorne's IDC sir!"

John nodded, "Lower the shield." He told the man, walking down to the gateroom as he did just that.

When Lorne's team walked through the gate with a trolley full of equipment and no injuries John smiled in relief, "So the mission went well then?"

Lorne grinned, "You could say that sir, we definitely found a lot of stuff worth scavenging."

John chuckled, "Hey Lorne, I'm wondering if you could do me a favour. I popped in to check how Elizabeth was earlier today and she was in pretty bad shape, if she's still not feeling great when you get home take her to the Infirmary."

Lorne nodded, "I was planning to anyway sir, she seemed pretty sick when I left this morning."

John managed to give the man a small smile, "Thanks Colonel."

At that Lorne considered himself dismissed and headed off to his quarters to check on Elizabeth; once there he found her in a worse state than John had and without further ado helped her up and took her to the Infirmary.

Carson hurried over to them when they arrived, Elizabeth looked as terrible as she felt and Carson ushered Lorne to help him get her lying on a bed. He did a few tests and sighed, "She's dehydrated son. You better go wait whilst I get her set up on a drip."

Lorne nodded and headed to the other side of the Infirmary, with a quick nod to Dr Keller he sat himself down on a spare Infirmary bed and activated his radio, "Colonel Sheppard, I'm at the Infirmary with Elizabeth. Doc says she's dehydrated, he's making me wait while he sorts her out."

"_Did he say if she would be okay?"_

"No, but I think it will be alright, Beckett's good, he'll have her back to normal in a couple of days."

"_Yeah, lets hope so. Thanks for letting me know Colonel. Sheppard out."_

"Understood." Lorne muttered, more to himself than to anyone else if he was honest.

So much had happened in the last few days that this was such a surprise to come on top of everything else. There had been the argument, he was so ashamed about that, alcohol and Sheppard had never mixed well, so when he heard that they were meeting up secretly he lost it. The fact of the matter was that he didn't know what he would do if he lost Elizabeth and he knew he shouldn't have struck out at her the way he did, he knew it was wrong and he would feel guilty about it for a very long time.

Then this out of the blue. She had been fine this morning, Sheppard had even said so, they must have talked in the mess hall whilst he was still in his bed, hangovers and missions didn't go too well together either.

He sighed as he leaned against the wall and closed his eyes, she was gonna be okay, she _had_ to be okay. She was fearless leader Elizabeth Weir, nothing could touch her and she was gonna be okay. It was that argument that kept him going for the next few hours Carson made him wait.

**TO BE CONTINUED!!  
**


	6. Shocks & The Infirmary

**A Different Life**

**Chapter 6**

"Hey, how are you feeling?" Evan Lorne asked his fiancée with a smile, he had been forced to wait a few hours so that Carson could run tests just to make sure everything was fine with Elizabeth and he was relieved to see her looking much better.

However, it appeared she didn't feel better because her reply was a groan, "Awful. Why am I in the Infirmary?"

"You were pretty sick last night so I brought you here, Carson said you were dehydrated. He asked if you had been sick and I told him you had, he said something about not being able to keep any fluids in your body." Evan explained to the exhausted woman, who only nodded and yawned in response.

"I suppose John put you up to this, he threatened to have Carson see me earlier." She told him, hoping he wouldn't be angry that John had been with her whilst he was away, but he only nodded, "Yeah and you shoulda let him, you would have got this sorted out sooner."

Carson walked over to them before Elizabeth could protest any further that she had been fine that morning. He smiled at the couple and said, "Well, Elizabeth, I know why you've been a bit ill lately."

Elizabeth frowned, "I thought it was just dehydration?" She asked the Doctor.

Carson nodded, "Oh yes it was. The dehydration was caused by the sickness though. Congratulations, you're pregnant."

Elizabeth's jaw dropped, "I'm what?"

Carson chuckled, "Pregnant lass. Well I'll leave you two alone." He gave them a warm smile and walked away from their little corner of the Infirmary.

Evan turned to her, as shocked as she herself was, "We're gonna have a baby." He stated in disbelief.

"Wow, I can't believe this… We didn't plan it at all, how did this happen?" Elizabeth asked, muttering to herself rather than talking to Evan, but he answered her question anyway.

"I don't know, something must have happened. Are you happy?" He asked her, feeling a little worried now about the concerned look on her face.

Elizabeth sighed, "Um yes, just shocked that's all. We aren't even married, it's all so sudden."

Evan opened his mouth to speak when someone called him on his radio, "2 secs. Lt Colonel Lorne?"

"_Hey Lorne, sorry for the early morning call, is Elizabeth doing all right now?"_

"Oh hey Sheppard, Yeah, she's fine. She'll be back at work in a couple of days."

"_That's good, hope she feels better soon. Thanks Colonel. Sheppard out."_

Evan turned back to Elizabeth, "It was Sheppard, he was asking how you were."

Elizabeth nodded her acknowledgement and then a light bulb inside her head turned on, "Evan I'm feeling really tired, why you don't go check on the city."

Evan nodded, "Will do." He walked to the door, but turned around when Elizabeth called him, "Oh and Evan, don't tell anyone yet."

With another nod he was gone. Elizabeth sighed and asked a nurse if she could ask Carson to come over, a few seconds later Carson was by her side, "What is it Elizabeth? Do you feel okay?"

Elizabeth sighed, "Carson…I know you have the technology and I know you've used it before, it's harmless and it works so I need you to carry out a test for me."

Carson frowned, "What kind of test?"

Elizabeth swallowed a lump that had suddenly swollen up in her throat, "I need to know who the father of the baby is."

Carson's eyes widened and Elizabeth silenced him with a motion of her hand before he could say anything else, "Yes, I feel horrible about it." She said quietly, answering his unsaid question. She continued, "I know you have the blood work of Evan and John, please run the test Carson."

"John? Elizabeth, what's going on?" He asked, sitting down on the end of Elizabeth's bed, "I'm not only the Doctor, I'm your friend and you can talk to me."

Elizabeth sighed, she wished Carson didn't have to ask her so many questions, "It was a mistake okay Carson, it shouldn't have happened and Evan doesn't know so I really need you to run that test."

The look in her eyes must have shown Carson how desperate she was because he nodded, "Alright. It won't take long."

She managed to muster up a small smile, "Thank you Carson."

With another sigh Elizabeth settled back down into her pillows, hoping against all hope that the baby would be Evans. If it wasn't she had no idea what to do with herself, she considered running off and living with the Athosians as a good way to go about things…

"Hey skiver." A cheeky voice said, causing her to look up and see a smiling John approach her, seeing him made her freak out even more about the whole baby thing, but she managed to put a fake smile on for him.

"Hey you know me, if Carson would let me I would be back at work today, I feel fine." She told him, which was pretty much true. Physically she felt fine, but mentally she felt so confused and frustrated that to put it simply, her brain hurt.

John sat down on the edge of her bed, "Good, works not the same without you. Oh, Rodney blew up the entire 6th level of the tower by the way." She opened her mouth, probably to yell at him, but John held up a hand and continued, "But we got our little replicater pal…what's his name Liam?"

"Niam." Elizabeth corrected, talking about the replicater they kept in a special anti-replicater cell down in the Atlantis dungeons.

"Ah that's it. Yeah Niam, we got him to fix it for us." He finished with a smile.

Elizabeth frowned, "What did you give him in return?"

John shrugged, "Rodney told him some stuff about ascension and he was happy enough to help us out and yes before you ask, I checked all the systems for a replicater virus, Radek found one and debugged it."

Elizabeth opened her mouth to speak again, but once again John stopped her, "And I sterilised the whole tower so that there was no way of him communicating with any other rogues that we didn't get in the big blast." Once he had finished telling her all of this he grinned, seeming very proud of himself.

Elizabeth gave him a real smile this time, "Great. Thanks John."

He nodded, "It is my job, well at least it is whilst you're not well. So where's the other half today then?"

Elizabeth replied, "Evan just went off to make sure everything was going smoothly in the city."

John nodded again, "Hey, Elizabeth. Are we ever gonna talk about what happened before or are we just gonna forget it ever happened?"

Elizabeth's face hardened, "Nothing ever happened John and nothing can ever happen again. I'm getting married in 2 months."

John nodded, "I understand well I-"

"Elizabeth, I have those test results - Oh Colonel Sheppard, hello there." Carson said, his face turning from sombre to shocked, John understood why he was shocked; he and Elizabeth had barely spoken in the past few weeks.

John smiled and said hello to Carson before saying that he was actually just leaving and with a smile to Elizabeth he left the Infirmary.

Elizabeth anxiously turned to Carson, "You got the results Carson?" She asked.

He nodded, "Aye. Elizabeth and it's bad news for you I'm afraid. The baby is Colonel Sheppard's."

Elizabeth's heart sank at those words, "You're positive Carson?" She asked quietly.

Carson nodded, "I ran the test twice to be sure." He told her, looking slightly concerned, "Will you be okay Elizabeth?"

She nodded, "I'll be fine Carson. I just need, I just need some time alone."

Carson said he understood and headed back to his office, leaving Elizabeth alone with her thoughts. How would she tell Evan? She would have to tell Evan. She couldn't wait until the baby was born and hope everything would be okay, what if it was a boy and it looked like John or a girl that had Johns eyes? She sighed loudly in frustration. Her life was a mess, all because of one mistake. A mistake that wasn't even a mistake, she didn't think that sleeping was John had been a mistake, it felt more right than sleeping with Evan did.

Elizabeth could feel her stomach tighten into a knot as she realised that all she could do now was tell Evan the truth. It would be difficult and there was no way their relationship was survive the argument that followed, but it was all that could be done.

She was just beginning to ponder when Carson would let her go, after all there was nothing wrong with her, when Evan came over smiling, "Hey, Doc says you're good to go. Although you shouldn't really be working, but you are allowed as long as I'm with you. Docs orders."

Elizabeth smiled forcefully, "Okay, let me get changed and I'll meet you outside."

He nodded and left, she tried very hard not to audibly groan, the last thing she needed right now was having to spend the whole afternoon with Evan, she knew she was going to have to tell him at some point, sooner rather than later.

Once she had changed she went out to the Infirmary waiting room and met Evan, who greeted her with a smile and slipped his hand into hers, "You glad to be going back to work?"

"Yeah, I hate being cooped up in the Infirmary." She said quietly. Evan watched her suspiciously and she knew he could tell there was something wrong with her. However he didn't say a thing, at least not until they reached her office.

Not that it made a difference, her office was about as private as the mess hall, it was made of glass and it didn't even have a door.

Despite this once Elizabeth had sat down behind her desk Evan sighed, "What's wrong Elizabeth? I can tell your keeping something from me."

Elizabeth bit hard on her lip, so hard that she nearly drew blood. Her heart pounded in her chest and her palms became sweaty, "Evan, it's about the baby."

Evans eyes grew wide, "Is it okay? Is something wrong with it?"

Elizabeth shook her head, looking guiltily down at the table, "No, the baby is fine. It's just that… I had Carson run some extra tests and the baby…it's…it's not yours."

She finished, swallowing hard and waiting for a roar of rage. Instead there came a quiet and very hurt, "What?"

Elizabeth kept staring at the desk, she couldn't bring herself to look into his eyes, not if they were filled with the same pain and hurt as his voice was, "3 days after John came back something happened between us that shouldn't of and the baby…it's his."

The yell of rage came now, she had been expecting it, but it didn't make it any easier to hear.

"SHEPPARD? ELIZABETH I TRUSTED YOU! YOU SWORE THAT EVERYTHING BETWEEN YOU AND HIM WAS IN THE PAST AND I BELIEVED YOU! I BET YOU TWO HAVE BEEN LAUGHING AT HOW MUCH OF A FUCKING IDIOT I AM HAVENT YOU?!"

He was screaming at her now and she had tears running down her face, "It wasn't like that Evan. It shouldn't have happened and it didn't again."

The entire control room was watching with rapt attention now and several more people were coming up from other levels of the tower to watch. Evans yells had probably been heard as far down as level 10.

He turned around and started to walk angrily up and down her office, processing this fact, "Well I suppose that's the wedding off then isn't it!"

Elizabeth could only manage to give him a small watery nod in response and he yelled again punching the only non-glass wall in the office so hard he made a dent in it and cool air from outside drifted into the room.

"I'm sorry Evan." She said quietly, knowing it wouldn't make a difference, but she daren't fight back. Evan could scare her when he got as mad as he was now.

"Sorry? You think sorry makes it all ok Elizabeth? You slept with the one guy you swore was in your past! After me trusting you when you told me that you loved me. Do you even love me?" He asked, quietly, but just as dangerously as if he had been shouting.

Elizabeth nodded, "I do Evan."

He turned his back to her, "I need to know one thing and god Dammit if you don't answer this honestly. Do you love him more than me? Tell me the truth Elizabeth."

He said turning back to the woman he thought he loved. She had tears streaming freely down her face now and she caught his eye for the first time since they had entered the office.

She gazed straight into his eyes and choked back a sob, "Yes." She told him quietly.

He didn't yell, he didn't say anything. He just nodded and looked down at the finger which bore her engagement ring.

As she pulled the ring from her finger she felt a painful tug at her heart. She put the ring down on the desk and he snatched it up. Without looking back once he left the office and stormed away through the control room.

Elizabeth watched the space where she had last saw him for a few moments, in disbelief and shock at what had happened. She knew it was going to play out the way it did, but it didn't make the pain any easier and she felt the now familiar tug in her stomach telling her she was going to be sick. She hurried out of the control room and down one level to her quarters, praying that Evan wouldn't be there.

She was in luck because he happened to be out, she locked her quarters from the inside and hurried to the bathroom. She didn't feel dehydrated anymore and she doubted the sickness was related to the pregnancy at all this time, it was the pain she felt from the argument and the loss of her fiancée. Well, so she thought.

She didn't know how long she sat there on the bathroom floor for, but soon the light had faded away and she found herself sitting in darkness. It was then she heard the door open, it had to be Evan. No one else's bio-signatures could unlock the door.

She froze as he searched the room for her, calling out, "Lizzie Lizzie. Where are you Lizzie?"

She bit her lip, he was drunk and with the argument that they had just had, she did not want him to find her whilst he was drunk. She quickly looked around the dark room for an escape route, finding none other than the tiny window that dropped straight into the ocean she realised if she couldn't escape she would have to hide.

She looked around the tiny bathroom and bit back a sigh when she came to the conclusion that she was screwed, the only place that looked as if it could hide anything in here was the bathroom cupboard and there was no way she would fit in there.

She considered radioing Rodney or John for help, but knew that if she did Evan would hear her. If she sat here silently for long enough maybe he would think she was staying at Laura and Rodney's and give up. Then she could sneak out whilst he was asleep.

Her luck was out tonight though. Not longer than a second after her hopeful thought she heard footsteps approach the bathroom door and watched the door handle turn. He opened the door slowly and although it was dark she could see him grin when he saw her sitting on the bathroom floor.

He grabbed her and pulled her into the bedroom, "Well Lizzie. Were you hiding from me? I wonder what would make you want to do that."

Elizabeth had put on her façade again, she knew Evan was going to hurt her, but she would not let him see her weakness, "I wasn't hiding Evan. I was in the bathroom because I felt sick."

Evan leered at her, "Oh that's Sheppard Juniors fault then isn't it? Not mine, oh no of course it's not my fault. It would have been my baby if you hadn't gone and FUCKED SHEPPARD!"

Elizabeth took a step back out of instinct as he glowered over her and yelled the end of his sentence. He chuckled, "Fearless leader Doctor Weir is scared of something after all then, and you damn well better be. You are going to get what you deserve, you dirty cheating BITCH!"

His voice rose as he became angrier again and Elizabeth now felt terrified, he had definitely drank more than the amount Carson told him was safe for his anger management issues and he would beat her to death if no one stopped him.

Evan took another step towards her and she suddenly had an idea, it would involve her getting a little bit hurt, but it would stop him from killing her. She pretended to be pushing her hair behind her ear and clicked her radio on, "Evan, you don't wanna do this. It's the alcohol that's talking."

From where John sat in the mess hall with his team he frowned, "You picking this up?" He asked them pointing to their headsets.

Only Rodney nodded, "What do you think is going on?"

John shook his head, "I don't know, but I don't think it's good."

"_You're going to pay for this Elizabeth. Oh trust me, you will pay."_

Rodney's eyes widened as he looked at John and they jumped out to rush to Elizabeth and Evan's joint quarters. They had gotten as far as the door of the mess hall when they heard Elizabeth's plea for help come through the radio.

"_John, get here quickly or he's going to-" _

Her voice cut out and Lorne yelled angrily at her, then there was a scream. John and Rodney immediately broke into a run, radioing for help along the way.

"Carson, its McKay we need a medical team at Elizabeth's quarters now!"

"_What? Rodney what's happened?"_

"Just hurry Carson!"

They picked up a little more speed.

"Bates, its Sheppard. Have a security team outside Lorne and Elizabeth's quarters now!"

"_I'm on it sir."_

By the time the two most important radio calls were sorted out the two friends were outside Elizabeth's quarters.

John made to go in, but the door was locked from the inside and neither he nor Rodney could open it, "Dammit. McKay can you manually get the door to open?" John asked, his worry clearly shining though his professional act.

Rodney shook his head, "It can only be opened by Lorne or Elizabeth or by a scientist in the control room. Even then I'm the only one who's managed it so far-"

John had stopped listening when Rodney mentioned a scientist and the control room. He was on the radio to Dr Zelenka, "Zelenka, are you in the control room?" He asked quickly.

"_Yes, why do you-"_

"I need you to get the door to Elizabeth and Lorne's quarters open and fast!"

"_But Rodney is the only person who has successfully done so. I could never-"_

"Rodney has faith in you Radek, at least try."

"_He does? Really? Okay I will do my best Colonel."_

John turned to Rodney anxiously, "Do you think he can do it?" He asked his friend quietly, Rodney sighed, "I don't know. Hopefully."

They could only hear silence coming from inside the room and this just made their fear mount.

A few seconds later Carson and a medical team rushed into the corridor, "What is it? What happened? Where is the casualty?"

John pointed to the door of the quarters, "Elizabeth radioed for help, we heard Lorne yelling and her screaming. He's hit her in the past and if he's drunk…" John trailed off and clicked his radio, "C'mon Radek. How's it coming?"

"_I have almost completed the override program Colonel, I only need a few more minutes."_

"Understood. Hurry it up if you can."

Carson began to say, "Son, we need to get her out of there as soon as possible. If he's hit her it could kill the-"

But before he could finish the security team consisting of Bates, Ronan, Teyla and a few young marines had rounded the corridor, "What's going on sir?" He asked, looking at the medical team and the locked door.

John turned to the team, "Set your gun to stun Ronon and when Zelenka gets that door open if Lorne is conscious stun him and get him to a cell downstairs as soon as you can."

Ronon nodded and set his gun to stun, Bates was not so easily won over, "Why are we shooting our own man sir? What has Colonel Lorne done?" He asked his commanding officer suspiciously.

John narrowed his eyes at the man, "We're pretty sure he's beaten Elizabeth unconscious, that a good enough reason for you to lock him up?"

Bates didn't reply and just when John was starting to get really pissed off, a voice in his ear gave him hope.

"_Okay Colonel. I think I have it."_

There was a hiss and the door slid open, "Go!" John yelled to the security team who rushed into the room with their guns at the ready, only to find Lorne unconscious on the floor.

John ordered Bates and his team to take the man down to a cell and lock him up and once assured it was safe rushed the medical team in to tend to Elizabeth.

Carson quickly checked her, "She's bleeding and she's got a concussion. We need to get her to the Infirmary ASAP!" he yelled to his team who lifted her onto a stretcher and hurried down the corridor to the Infirmary. John and Rodney followed the team and proceeded to get very annoyed with the nurse who forced them to wait outside until Elizabeth was given the okay to have visitors.

John kicked the wall, "That bastard! Why the hell did that bastard do that to her?! I swear to god I am going to kill him!"

Rodney rolled his eyes, "Sheppard, I'm worried about Elizabeth too, but killing Lorne isn't going to help her right now."

John shot a glare Rodney's way, "Yeah well, it would make me feel better." He said as he began to pace the waiting room once more.

"_Colonel Sheppard?"_

John sighed as a voice came through his radio, he tried his best to calm himself before replying, "What is it Bates?"

"_Colonel Lorne is awake sir."_

"Has he said anything?"

"_No sir, he just keeps asking how Dr Weir is."_

"Are you with him right now?"

"_No sir, Teyla and Ronon are in there with him."_

"Understood. Keep him there until I have time to come and speak to him myself."

"_Understood. Sir, is Dr Weir going to be okay?"_

"Lets hope so Sergeant. Sheppard out."

"_Copy that sir. Bates out."_

Rodney gave him a half amused, half worried look, "So your not gonna rush down there and kill him then?"

John shook his head, "Nah. I wanna make sure Elizabeth's alright first. Then I'll rush down there and kill him."

Rodney chuckled. He knew fine well the man was joking, Sheppard would never kill a man of his own team, but he did know that he would exhaust his vocal cords shouting at the man.

Whilst in the Infirmary Elizabeth lay in bed, looking pretty bashed up. She had a bruise on her cheek and a few more on her neck and arms from where Evan had grabbed her so tightly.

Carson sighed as he looked down at the sleeping woman whom he had come to love like a sister and wondered how such a strong, brave person had let herself be in such a terrifying relationship. The only person Elizabeth had talked to about the violence was Kate, who knew that the violence had only begun when Colonel John Sheppard returned. Things had gone downhill for the couple since that day, before it had happened they had been inseparable and very much in love, so it seemed. Then again you never did know what went on behind closed doors.

After an hour he finally let Rodney and John into the Infirmary, but warned them first that she probably wouldn't be awake for a few hours and told them that they couldn't stay long.

They walked over to her bedside and John muttered angrily to himself as he saw the bruises the man who claimed he loved her had given her. Even Rodney sighed and dismissed himself. You heard about stuff like this all the time, but you never thought it would or could affect you or someone close to you, so it hit him nearly as hard as it had hit John.

He took Elizabeth's hand in his own and squeezed it tightly, to comfort not only her, but himself, "It's going to be okay Elizabeth. I'm not going to let him hurt you again." He whispered as he looked down at her bruised face and winced, how could a man do something like that to such a beautiful woman? He didn't think he would ever understand it.

**TO BE CONTINUED!**


	7. Rage & Fear

**A Different Life**

**Chapter 7**

Elizabeth didn't know what was happening or where she was, all she could feel was a throbbing pain in her head. She couldn't open her eyes, but she could hear chatter all around her, she tried to lift her eyelids, but they were so heavy and she felt as though her head might explode.

Carson had been in the middle of telling John for about the 10th time that night to go back to his quarters and get some sleep, when he saw Elizabeth try to open her eyes, "Elizabeth, keep your eyes closed just now. You got a bit of a concussion last night. I'm going to give you some medicine for the pain."

He tapped a few things on his computer and gave her more pain medicine. Elizabeth slowly began to feel slightly more aware and opened her eyes warily. The Infirmary was very dark, with the lights dimmed right down and barely any moonlight streaming through the window. She frowned as she saw John sitting at her bed, "What happened?" She asked him hoarsely.

He handed her a glass of water and she rewarded him with a grateful smile, "We were hoping you could tell us Elizabeth. We found you unconscious in your quarters; Lorne hit you again didn't he?"

Elizabeth's frown deepened as she remembered the night before, "Yes, we had an argument and he lost control…"

Carson replied, "You have a pretty big bruise on your side, I think you hit into the bed when you fell over."

Elizabeth just gave a small shake of her head as Carson walked away and she held up her hand to the small stream of moonlight coming from the window behind her, "Hm, no engagement ring."

John's eyes lit up slightly, "The engagements definitely off?"

Elizabeth nodded, "Oh yeah, a fight like that and you think I would marry him?"

John sighed, "Yeah, he's an ass-"

"He has anger-management issues, he isn't supposed to drink, it's why he gets like that. Besides it was always gonna be over anyway. The fight was bound to come at some point." She told him, rubbing her forehead as the now smaller headache pounded away.

"What did you fight about you?" He asked with a frown and she chuckled, "You."

"Again? Did he find out about that night?" John asked, leaning forward and talking quieter.

Elizabeth nodded, "Yeah and from the way he yelled about it in my office I think most of the city did so there's no need to whisper."

John chuckled, "Well, cats out the bag I suppose. I'm just glad that you just bumped your head and got a few bruises, so much worse things could have happened tonight if-"

Elizabeth cut him off as her eyes widened in horror, "Carson!" She called as quietly as she could to be heard by the man standing at a bed a little away from hers. He quickly came over to see what the matter was and she seemed to forget John was there, "Carson, you said I hit my side. What about the baby? Is the baby okay?"

"What? You're pregnant?! Does Lorne know?" John asked suddenly in shock and outrage.

Elizabeth ignored him and turned to Carson, "The baby is going to be fine Elizabeth." He told her softly and she let out a sigh of relief.

John however was not going to relent so easily, "Elizabeth does Lorne know about this?"

Elizabeth gave him a small nod and John let out a roar of rage, "He would stoop as low to hit a pregnant woman? That's it, I've had it. I'm going down there to deal with it myself."

"John!" Elizabeth shouted sternly at the man, "You are not going down in a state like this. I don't want any violence between expedition members! We're all in this together."

"Not when you hit bloody pregnant women, I'm sorry Elizabeth, but I am sending him somewhere far away from you. He is NOT staying here!" John told her angrily, but she knew he was angry at Lorne, not her. With that however he stormed from the Infirmary and Elizabeth let out a groan, why was her life so confusing?

John stormed through the corridors and curious whispers mounted with every level he went down. When he had eventually reached the lowest level of the 'Atlantis Dungeons' as Elizabeth had christened them he was fuming. These were the highest security cells in the city, even the Wraith hadn't been kept this far down.

John took a deep breath and steadied himself before stepping into the long corridor, he passed Niams cell with no bother, but got shouted at quite vigorously upon passing the Genii section of the cells where Sora & Kolya found themselves locked up.

When he reached Lorne's cell he decided to stay on the other side of the bars for minimum damage. "You realize there's no way you are staying in this city after what you did right?"

Lorne didn't look up, "Where are you going to send me?"

Johns glare burned right into him, "I've not quite decided yet, a planet with lots of bad guy's maybe…"

"Sheppard I know it was my fault for drinking more than my condition allows, but I really didn't mean to hurt her." Lorne told him quietly.

John frowned, he believed that Lorne was actually telling the truth, "I don't think you staying in Atlantis is a good idea with anger management issues as bad as that Lorne, you can cause damage to more than just Elizabeth."

"Carson almost has something that will help me, please can you give him a chance to at least try it out? I won't get in your way, you can have Elizabeth. She's wanted you all along anyway. I was just a stepping stone to help her heal when you were gone." Lorne didn't seem angry anymore, just disappointed and John genuinely felt sorry for him.

"Look I'm sorry about the way things played out between you two. I didn't mean to get in the way, it just sorta happened. I'll talk to Carson about the remedy he's coming up with and if it works you can stay in the city, but I'm thinking about putting you back to AR-2 I think the responsibility went to your head." John said calmly and genuinely.

Lorne nodded, "I just want to be able to stay here, it's my home now. I'll be fine and I won't be a hassle, you guys will be playing happy families in 9 months anyways." He chuckled, somewhat bitterly.

John sighed and waved his hand over the panel, he entered the cell and sat down opposite Lorne, "Look I don't know what's going to happen between me and Elizabeth anymore. We were engaged before and now everything's different, but even if something does happen that kid is still yours Lorne and if Carson can help you then I see no reason why you can't see it whenever you want."

Lorne frowned, "She hasn't told you? I have no right to see that kid when it's born Sheppard, it's not mine."

Johns frown mirrored Lorne's, "What do you mean it's not yours?"

"I think you and Elizabeth need to have a serious talk." He told the man sceptically.

John sighed, "Yeah, I'm with you on that one." He told Lorne before leaving the cell and hurrying back up 5 levels to the Infirmary.

However when he got there he found an empty Infirmary bed where Elizabeth had previously been, he was then informed by a nurse that Elizabeth had been released and was probably in her office.

So with a sigh he made his way up another 3 levels to the control room, when he got there he was stopped and bombarded with questions by Radek Zelenka and that technician guy he thought was called Chuck.

"What is happening to Colonel Lorne? Is he being sent away?"

John shrugged, "We don't know yet. Excuse me I really have to see Elizabeth." He told the crowd as he pushed his way through and saw Elizabeth sitting at her desk.

He made his way into her office, "I think we need to talk." He told her seriously.

"Sit down." She said with a slight frown as she motioned at the seat across from her.

"Okay I just had a very interesting chat with Lorne. First of all I'm thinking he is going to be able to stay if Carson can finish this drug that will help his anger management issues. He's a good soldier and I genuinely think he didn't mean it."

Elizabeth nodded, "I agree, although he knows he shouldn't drink that much, but if Carson can perfect the drug he should stay, so long as he wants too."

John narrowed his eyes, "He does. But here's the 2nd interesting thing, he told me that he wasn't the father of your baby and that I should talk to you. Care to explain what that's all about?"

Elizabeth sighed, he didn't seem annoyed so much, just confused, "Well he isn't the father. I had Carson run a few extra tests when I found out about the pregnancy."

"Because of what happened between us?" John asked her quietly.

Elizabeth nodded again, "Yes, naturally I was worried and the tests came back with the result that he wasn't the father."

"That's what the argument was about, that's why he got drunk and hit you?" John asked, although he already knew it must have been why they argued so violently.

Elizabeth nodded, "Yes, that's why we fought that day."

"So if Lorne isn't the father… that means that, I am?" John asked her, not so much in shock as he had suspected it from the moment Lorne had told him that the baby wasn't his. No the tone John took with her was more fear and slight anticipation. He didn't know what he thought about becoming a father, in all honesty the thought had never crossed his mind before.

Elizabeth fixed him with a determined stare and before she even answered he knew what the answer would be from that look in her eye, "Yes John. You are my baby's father."

**To Be Continued!**


	8. Love & Family

**A Different Life **

**Chapter 8**

It had been a week since the disastrous incident with Lorne and the confrontation with John. All it had taken was for John to confide in Rodney and by now the whole city knew that the leader was no longer engaged, but instead was pregnant. They also knew that the baby was John Sheppard's and Elizabeth had seen no point in hiding the fact that she cared about him any longer.

The city already knew and they didn't seem to care, her friends still loved her and her people still respected her. Everything she had feared she would lose when the news came out had turned out to be the worst case scenario in her head and wasn't the way things played out at all.

She hadn't openly begun a relationship with John, but after he had found out about the baby he had become quiet and withdrawn only to come out of his day-long depression as a man excited about becoming a father.

They hadn't spoken much about it since then because he had been pre-occupied with leading his first mission since he came back. He was away for 3 days and came back to give her the news that they had successfully brokered a treaty between the people of Andora, they would give them technology in return for food.

Elizabeth had congratulated him on the mission being a success and had sent him and the team off to shower and freshen up. Knowing that John was back in the city made Elizabeth both happy and nervous. She knew he was safe now, but she was anxious about the talk they were going to need to have now.

She was worried that he wouldn't want to be with her anymore despite his excitement about the baby, she didn't know what to do about Evan Lorne who was currently in the Infirmary being treated by Carson. Most of all though she had to choose between what she wanted and what would make her look good. She was the leader and appearances meant everything.

She wanted to begin a relationship with John, like they had before he left, but they could be open about it now. She wanted them to be happy together and start their family together. However she worried about what Evan would think if she dated him so soon after their break-up and would the rumour mills and the people in the city who respected her would think. Would they understand? Or would they hate her?

With so many questions whirling through her mind she had no idea what to do and that scared her.

Elizabeth knew that she had to have her mind made up before she went to John's quarters and as she stood to leave her office the anxiety set in once more.

She told Chuck that she was going for a walk and that she had her radio if he needed her. The man smiled and bade her have a good walk. She made her way through the city hallways on her way to John's quarters and she felt the gaze of so many people watching her as she did so.

Some said 'Hello' or nodded with a 'Ma'am' and some just stared at her like she was some sort of creature in a zoo to be gawked at. She kept her head held high and didn't let them know how much their constant staring affected her and it was with a sigh of relief that when she reached the corridor where Johns quarters were it was deserted.

She rang the bell by swiping her hand across the panel and looked around anxiously to make sure no one was coming along the corridor. When the door slid open revealing John standing there in a pair of casual joggers and the old baggy T-Shirt he used to let her sleep in she didn't wait to be invited into his quarters, she just hurried in before anyone could come along the corridor.

The door slid shut and she turned to look at John who was watching her in amusement "A little bit jumpy?" He asked cheekily and she found herself rolling her eyes, "Well I did get stared at the whole way down here, your quarters are too far away from my office."

He chuckled as he moved across the room to sit down on his bed, "Sorry for the inconvenience." He said sarcastically.

She smiled weakly at him, "I came here to talk to you." She stated a little dumbly. Why else would she be here? She thought to herself.

John didn't laugh at her however he just smiled, "I thought I would get a visit from you soon. You don't know what to do."

She sighed, he knew her too well, "Yeah, I know what I want to do, but whether or not I should do it is a different story."

He smiled knowingly at her, "You want to follow your heart, but the whole time you've been here you've been told to follow your head and now you don't know which one is right."

She glared at him playfully, "Would you stop doing that?" It would have been convincing if she hadn't smiled and given herself away.

John shrugged playfully at her, "I have no idea what you're talking about."

His comment reminded her of a time when they were just friends blindly in love, back when things were simple and it made her laugh at the memories that flooded back to her. She knew then what she had to do.

"So where are we? What are we?" She asked the man seriously, all traces of their light-hearted banter gone.

"Where do you want us to be?" John asked her quietly and as he looked in her eyes she could see the uncertainty written all over his face, he was afraid she would reject him.

She swallowed hard, but looked him in the eye as she spoke, "I want us to be a family, I want us to raise this baby together as a family."

He stared at her sombrely for a moment and said, "I'm sorry Elizabeth, but I can't do that."

Her face dropped and she was about to turn around to leave when she saw his face spread into a grin, he jumped up from the bed and pulled her into a hug, "I'm kidding Elizabeth, I want that too." She whacked his arm in fake annoyance as he hugged her and let out a breath she hadn't realised she was holding.

"You nearly gave me a bloody heartache!" She said into his chest and he grinned, "Sorry about that, I couldn't resist." He pulled back from the hug and kissed her on the forehead, "As if I could ever say no to you."

She smiled slightly, "I know we've gone through a lot of crap since you came back John, but you do know that I love you, don't you?"

He smiled back at her, "Of course I do and you know that I feel the same way."

She breathed a sigh of relief and her features visibly softened as all traces of anxiety left her face.

However part 2 of their discussion was yet to be mentioned and John felt that since Elizabeth had started, he would bring up the other issue that needed to be discussed.

"So is this official or would you rather keep it a secret? I think I know what the answer is considering you snuck to my quarters." He smiled at her, but she could see that underneath the smile he wanted everyone to know how much he loved her because now they could know and before he left they couldn't.

The look of longing in his eyes won over Elizabeth's worry of what people would think about the situation and she smiled genuinely at him, "It's not a secret. Everyone knows that there has been something between us for a long time, there isn't any point in keeping it a secret."

He grinned at her and the look of happiness on his face was enough to make her heart melt, unable to resist she pulled him into a kiss that said everything they couldn't say to each other, the things they couldn't verbalise, at least not yet anyway.

When Elizabeth pulled back from the kiss John grabbed her hand and led her out of his quarters with a grin. She asked where they were going, but he wouldn't tell her and he didn't drop her hand either.

As they walked through the city hundreds of eyes watched them with curiosity and whispers followed them until they reached a place on one of the lower towers that only she and John knew about. The corridors leading to it were deserted.

It was so much better than a balcony. The circular tower had a roof, but underneath the roof was a large circle room, it was empty and had barriers all around the edge. John was sure it had once been a viewpoint for when the Lantians were not as developed and used boats rather than ships. You could see the city from every angle and the place was spectacular.

John walked to the middle of the room and beckoned for her to follow, she walked over to him and as they stood there with the cool sea breeze drifting over them Elizabeth felt completely calm for the first time since John had returned.

John grinned at her and when he began to go down on one knee she knew what he was doing. He pulled the engagement ring he had given her a week before he left on the suicide mission and said, "Elizabeth Weir, I love you and always will so will you do me the honour of agreeing to marry me, again?"

Elizabeth laughed as he added 'again' as an afterthought and her grin matched his, "Of course I will!" She said as he slipped the ring onto her finger. For the first time in a long time the ring on her wedding finger didn't feel like a heavy weight pulling her down, it made her feel lighter and carefree as she enveloped John in a hug.

She knew that although the past few weeks had been hard everything was falling into place now. All she could hope for was that things would stay that way, she had suffered so much up until now and she would like to think that she deserved a happy ending.

**The End =]**

**A/N- I am SO sorry that it took me so long to finish this, but i went off SGA for a while and neglected my SGA fics. I know its an abrupt ending & i had intended to do more chapters than this, but this seemed like a good place to end it and if i tried to drag it on i think it would be a disaster so i hope you enjoyed this fic and if any of you are reading my other unfininished SGA fics then you can expect an update on them soon!**

**Thank You all for reading & reviewing and putting up with the huge gaps between updates! x  
**


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